1XPY Isomerase date Oct 10, 2004
title Structural Basis For Catalytic Racemization And Substrate Sp Of An N-Acylamino Acid Racemase Homologue From Deinococcus Radiodurans
authors W.C.Wang, W.C.Chiu, S.K.Hsu, C.L.Wu, C.Y.Chen, J.S.Liu, W.H
compound source
Molecule: N-Acylamino Acid Racemase
Chain: A, B, C, D
Engineered: Yes
 Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Jm109
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Naaar-Pqe30
symmetry Space Group: P 4
R_factor 0.171 R_Free 0.227
crystal
cell
length a length b length c angle alpha angle beta angle gamma
116.159 116.159 120.426 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand MG, NLQ enzyme
related structures by homologous chain: 1R0M, 1XS2
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceStructural basis for catalytic racemization and substrate specificity of an N-acylamino acid racemase homologue from Deinococcus radiodurans., Wang WC, Chiu WC, Hsu SK, Wu CL, Chen CY, Liu JS, Hsu WH, J Mol Biol 2004 Sep 3;342(1):155-69. PMID:15313614
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (243 Kb) [Save to disk]
  • Biological Unit Coordinates (1xpy.pdb1.gz) 120 Kb
  • Biological Unit Coordinates (1xpy.pdb2.gz) 121 Kb
  • LPC: Ligand-Protein Contacts for 1XPY
  • CSU: Contacts of Structural Units for 1XPY
  • Likely Quarternary Molecular Structure file(s) for 1XPY
  • Retrieve 1XPY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1XPY from S2C, [Save to disk]
    • View 1XPY in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 1XPY
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1XPY, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1xpya1, region A:133-375 [Jmol] [rasmolscript] [script source]
        - Domain d1xpya2, region A:6-132 [Jmol] [rasmolscript] [script source]
        - Domain d1xpyb1, region B:133-375 [Jmol] [rasmolscript] [script source]
        - Domain d1xpyb2, region B:6-132 [Jmol] [rasmolscript] [script source]
        - Domain d1xpyc1, region C:133-375 [Jmol] [rasmolscript] [script source]
        - Domain d1xpyc2, region C:6-132 [Jmol] [rasmolscript] [script source]
        - Domain d1xpyd1, region D:133-375 [Jmol] [rasmolscript] [script source]
        - Domain d1xpyd2, region D:6-132 [Jmol] [rasmolscript] [script source]
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1xpy_C] [1xpy_D] [1xpy_A] [1xpy_B] [1xpy]
  • SWISS-PROT database: [Q9RYA6]
  • Domain organization of [Q9RYA6_DEIRA] by SWISSPFAM
  • Domain found in 1XPY: [MR_MLE ] by SMART
    • Other resources with information on 1XPY
  • Community annotation for 1XPY at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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